The Brazil nut is a highly valuable non‐timber forest product from a wild, hyperdominant, emergent tree species that is increasingly vulnerable and exposed to habitat degradation. We provide evidence for how Brazil nut genetic resources are negatively affected by forest degradation and discuss the consequences of this for reproductive success. To avoid negative effects of genetic erosion and inbreeding, we discuss the need to cease large‐scale forest conversion and to promote landscape connectivity. This could support gene flow, maintain genetic diversity across individuals reproducing in clustered patterns and contribute to securing the long‐termed reproductive viability and resilience of this high socio‐economically and ecologically valuable species.